{"id":"https://openalex.org/W4405363302","doi":"https://doi.org/10.1371/journal.pcbi.1012669","title":"Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding","display_name":"Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding","publication_year":2024,"publication_date":"2024-12-13","ids":{"openalex":"https://openalex.org/W4405363302","doi":"https://doi.org/10.1371/journal.pcbi.1012669","pmid":"https://pubmed.ncbi.nlm.nih.gov/39671444"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012669","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012669","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012669&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012669&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043658274","display_name":"Pengyu Liu","orcid":"https://orcid.org/0000-0001-7154-7546"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pengyu Liu","raw_affiliation_strings":["Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026077144","display_name":"Jacob Lusk","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jacob Lusk","raw_affiliation_strings":["Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083450874","display_name":"Nata\u0161a Jonoska","orcid":null},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nata\u0161a Jonoska","raw_affiliation_strings":["Department of Mathematics and Statistics, University of South Florida, Tampa, Florida, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of South Florida, Tampa, Florida, United States of America","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087620774","display_name":"Mariel V\u00e1zquez","orcid":"https://orcid.org/0000-0001-8328-6806"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mariel V\u00e1zquez","raw_affiliation_strings":["Department of Mathematics, University of California, Davis, Davis, California, United States of America","Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of California, Davis, Davis, California, United States of America","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5026077144","https://openalex.org/A5043658274","https://openalex.org/A5083450874","https://openalex.org/A5087620774"],"corresponding_institution_ids":["https://openalex.org/I2613432","https://openalex.org/I84218800"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6869,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.71274558,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"20","issue":"12","first_page":"e1012669","last_page":"e1012669"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6562111377716064},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5755428075790405},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5617520809173584},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.49289894104003906},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4811771810054779},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.431873619556427},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.42199164628982544},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4214746356010437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35777348279953003},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.355028361082077},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.32690149545669556},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2940559983253479},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2578749358654022},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10098212957382202}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6562111377716064},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5755428075790405},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5617520809173584},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.49289894104003906},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4811771810054779},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.431873619556427},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.42199164628982544},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4214746356010437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35777348279953003},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.355028361082077},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.32690149545669556},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2940559983253479},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2578749358654022},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10098212957382202},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000080870","descriptor_name":"R-Loop Structures","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000080870","descriptor_name":"R-Loop Structures","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000080870","descriptor_name":"R-Loop Structures","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1012669","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012669","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012669&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:39671444","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39671444","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7hf1p79d","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7hf1p79d","pdf_url":"https://escholarship.org/content/qt7hf1p79d/qt7hf1p79d.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS Computational Biology, vol 20, iss 12","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11706388","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11706388","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11706388/pdf/pcbi.1012669.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:ark:/13030/qt7hf1p79d","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:02fdc0b530544f76a6eb90203fc77996","is_oa":true,"landing_page_url":"https://doaj.org/article/02fdc0b530544f76a6eb90203fc77996","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 12, p e1012669 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012669","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012669","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012669&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1590907431","display_name":"DMS/NIGMS 2: Collaborative Research: Modeling R-Loop Formation and Topology Using Braids and Graphs Coupled with Single-Molecule Footprinting","funder_award_id":"2054347","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2339798153","display_name":null,"funder_award_id":"DMS/NIGMS#2054321","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3247092932","display_name":null,"funder_award_id":"2107267","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3287280565","display_name":null,"funder_award_id":"DMS/NIGMS#2054347","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3407320189","display_name":null,"funder_award_id":"DMS#1764406","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3855887613","display_name":null,"funder_award_id":"CCF#2107267","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5632668192","display_name":"DMS/NIGMS 2: Collaborative Research: Modeling R-Loop Formation and Topology Using Braids and Graphs Coupled with Single-Molecule Footprinting","funder_award_id":"2054321","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5662594850","display_name":"Collaborative Research: DNA Packing of Bacteriophages: Liquid Crystal Modeling through Analysis, Knot Theory  and Numerical Simulation.","funder_award_id":"1817156","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5698481459","display_name":null,"funder_award_id":"1764406","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7223133011","display_name":null,"funder_award_id":"DMS#1817156","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7444898818","display_name":null,"funder_award_id":"594594","funder_id":"https://openalex.org/F4320306164","funder_display_name":"Simons Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306159","display_name":"W. M. Keck Foundation","ror":"https://ror.org/000dswa46"},{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405363302.pdf","grobid_xml":"https://content.openalex.org/works/W4405363302.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W129436484","https://openalex.org/W1967706132","https://openalex.org/W2070327606","https://openalex.org/W2105070391","https://openalex.org/W2124050695","https://openalex.org/W2158381555","https://openalex.org/W2314361409","https://openalex.org/W2340421620","https://openalex.org/W2463453322","https://openalex.org/W2534058863","https://openalex.org/W2749177415","https://openalex.org/W2774310835","https://openalex.org/W2796420015","https://openalex.org/W2888533280","https://openalex.org/W2921848211","https://openalex.org/W2938347885","https://openalex.org/W2944795562","https://openalex.org/W2951298881","https://openalex.org/W2952580394","https://openalex.org/W3007507416","https://openalex.org/W3033583573","https://openalex.org/W3043305774","https://openalex.org/W3048451018","https://openalex.org/W3081157667","https://openalex.org/W3161020364","https://openalex.org/W3164387821","https://openalex.org/W3166605709","https://openalex.org/W3184560454","https://openalex.org/W3213075371","https://openalex.org/W4210941983","https://openalex.org/W4226051476","https://openalex.org/W4226331860","https://openalex.org/W4280595454","https://openalex.org/W4309132320","https://openalex.org/W4317433806","https://openalex.org/W4318981890","https://openalex.org/W4320082227","https://openalex.org/W4322492219","https://openalex.org/W4362586475","https://openalex.org/W4394713878","https://openalex.org/W4402272852"],"related_works":["https://openalex.org/W3047450301","https://openalex.org/W2558432341","https://openalex.org/W1975806245","https://openalex.org/W2345156963","https://openalex.org/W1971402940","https://openalex.org/W2919479895","https://openalex.org/W2131054067","https://openalex.org/W3196523453","https://openalex.org/W2021868453","https://openalex.org/W2791545870"],"abstract_inverted_index":{"R-loops":[0],"are":[1,31,247],"a":[2,84,98,109,135,145,156,183],"class":[3,86],"of":[4,79,87,89,97,127,166,190,196,216,224],"non-canonical":[5],"nucleic":[6],"acid":[7],"structures":[8,30,130,154],"that":[9,45,111,176,203,236],"typically":[10],"form":[11],"during":[12],"transcription":[13],"when":[14],"the":[15,19,24,70,77,116,163,167,187,193,204,214,222],"nascent":[16,73,151],"RNA":[17,74,90,104,128,152,158,225],"hybridizes":[18],"DNA":[20,26,46],"template":[21],"strand,":[22],"leaving":[23],"non-template":[25],"strand":[27],"unpaired.":[28],"These":[29],"abundant":[32],"in":[33],"nature":[34],"and":[35,39,48,58,76,123,140,161,192,244],"play":[36],"important":[37],"physiological":[38],"pathological":[40],"roles.":[41],"Recent":[42],"research":[43],"shows":[44],"sequence":[47],"topology":[49],"affect":[50],"R-loops,":[51],"yet":[52],"it":[53],"remains":[54],"unclear":[55],"how":[56],"these":[57],"other":[59],"factors":[60],"contribute":[61],"to":[62,173,220],"R-loop":[63,142,178,197,211,230],"formation.":[64,198,231],"In":[65,232],"this":[66,171],"work,":[67],"we":[68,181,234],"investigate":[69],"link":[71],"between":[72,186],"folding":[75,159],"formation":[78,143],"R-loops.":[80,250],"We":[81,133],"introduce":[82],"tree-polynomials,":[83],"new":[85],"representations":[88,165],"secondary":[91,105,129,153,226],"structures.":[92,168],"A":[93],"tree-polynomial":[94,164],"representation":[95],"consists":[96],"rooted":[99,117],"tree":[100],"associated":[101,228,248],"with":[102,108,115,229,238,249],"an":[103],"structure":[106,227],"together":[107],"polynomial":[110],"is":[112],"uniquely":[113],"identified":[114],"tree.":[118],"Tree-polynomials":[119],"enable":[120],"accurate,":[121],"interpretable":[122],"efficient":[124],"data":[125],"analysis":[126],"without":[131],"pseudoknots.":[132],"develop":[134],"computational":[136],"pipeline":[137,149,172,205],"for":[138,209],"investigating":[139],"predicting":[141],"from":[144,155],"genomic":[146],"sequence.":[147],"The":[148],"obtains":[150],"co-transcriptional":[157],"software,":[160],"computes":[162],"By":[169],"applying":[170],"plasmid":[174],"sequences":[175],"contain":[177],"forming":[179],"genes,":[180],"establish":[182],"strong":[184,200],"correlation":[185,201],"coefficient":[188],"sums":[189],"tree-polynomials":[191,217],"experimental":[194],"probability":[195],"Such":[199],"indicates":[202],"can":[206],"be":[207],"used":[208],"accurate":[210],"prediction.":[212],"Furthermore,":[213],"interpretability":[215],"allows":[218],"us":[219],"characterize":[221],"features":[223],"particular,":[233],"identify":[235],"branches":[237],"short":[239],"stems":[240],"separated":[241],"by":[242],"bulges":[243],"interior":[245],"loops":[246]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
